10-106422755-A-G

Position:

• chr10-106422755-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.642 in 151,842 control chromosomes in the GnomAD database, including 32,127 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (32127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97330 AN: 151722 Hom.: 32089 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.654

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.642 AC: 97426 AN: 151842 Hom.: 32127 Cov.: 32 AF XY: 0.639 AC XY: 47389 AN XY: 74178

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.651

Alfa AF: 0.608 Hom.: 13458

Bravo AF: 0.650

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2418804; hg19: chr10-108182513;